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@OutisLi OutisLi commented Aug 10, 2025

Fix: support "max:N" and "filter:N" batch_size rules in DeepmdDataSystem

Problem

  • Using batch_size: "max:..." or "filter:..." in configs caused:
    • RuntimeError: unknown batch_size rule max during the PyTorch path (neighbor statistics).
  • Docs mention these rules and PyTorch DpLoaderSet already supports them, so behavior was inconsistent across layers.

Cause

  • The common data layer DeepmdDataSystem only implemented "auto" and "mixed" for string batch_size, missing "max" and "filter".
  • PT training performs neighbor statistics via DeepmdDataSystem before real training, so it failed early when those rules were used.

Fix

  • Implement "max:N" and "filter:N" in DeepmdDataSystem.__init__ to mirror DpLoaderSet semantics:
    • max:N: per-system batch_size = max(1, N // natoms) so batch_size * natoms <= N.
    • filter:N: drop systems with natoms > N (warn if any removed; error if none left), then set per-system batch_size as in max:N.
  • After filtering, update self.data_systems, self.system_dirs, and self.nsystems before computing other metadata.

Impact

  • Aligns the common layer behavior with PyTorch DpLoaderSet and with the documentation.
  • Prevents PT neighbor-stat crashes with configs using "max"/"filter".

Compatibility

  • No change to numeric batch_size or existing "auto"/"auto:N"/"mixed:N" rules.
  • TF/PT/PD paths now accept the same batch_size rules consistently in the common layer.

Files Changed

  • deepmd/utils/data_system.py: add parsing branches for "max:N" and "filter:N" in DeepmdDataSystem.__init__.
elif "max" == words[0]:
                # Determine batch size so that batch_size * natoms <= rule, at least 1
                if len(words) != 2:
                    raise RuntimeError("batch size must be specified for max systems")
                rule = int(words[1])
                bs = []
                for ii in self.data_systems:
                    ni = ii.get_natoms()
                    bsi = rule // ni
                    if bsi == 0:
                        bsi = 1
                    bs.append(bsi)
                self.batch_size = bs
            elif "filter" == words[0]:
                # Remove systems with natoms > rule, then set batch size like "max:rule"
                if len(words) != 2:
                    raise RuntimeError("batch size must be specified for filter systems")
                rule = int(words[1])
                filtered_data_systems = []
                filtered_system_dirs = []
                for sys_dir, data_sys in zip(self.system_dirs, self.data_systems):
                    if data_sys.get_natoms() <= rule:
                        filtered_data_systems.append(data_sys)
                        filtered_system_dirs.append(sys_dir)
                if len(filtered_data_systems) == 0:
                    raise RuntimeError(f"No system left after removing systems with more than {rule} atoms")
                if len(filtered_data_systems) != len(self.data_systems):
                    warnings.warn(f"Remove {len(self.data_systems) - len(filtered_data_systems)} systems with more than {rule} atoms")
                self.data_systems = filtered_data_systems
                self.system_dirs = filtered_system_dirs
                self.nsystems = len(self.data_systems)
                bs = []
                for ii in self.data_systems:
                    ni = ii.get_natoms()
                    bsi = rule // ni
                    if bsi == 0:
                        bsi = 1
                    bs.append(bsi)
                self.batch_size = bs

Summary by CodeRabbit

  • New Features
    • Added support for "max" and "filter" batch size rules, allowing more flexible control over batch sizing and filtering of data systems based on atom counts.
  • Bug Fixes
    • Improved error handling for incorrect batch size string formats and cases where no systems remain after filtering.

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coderabbitai bot commented Aug 10, 2025

📝 Walkthrough

Walkthrough

The batch size parsing logic in the DeepmdDataSystem.__init__ method was updated to support two new rules: "max" and "filter". The "max" rule limits the batch size per system based on atom count, while the "filter" rule removes systems exceeding a threshold and adjusts batch size accordingly. Error handling for invalid formats was added.

Changes

Cohort / File(s) Change Summary
Batch Size Rules in Data System
deepmd/utils/data_system.py
Added "max" and "filter" batch size rules to batch size string parsing in DeepmdDataSystem.__init__; implemented logic to compute per-system batch sizes and filter systems based on atom count; added error and warning handling for invalid cases.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant DeepmdDataSystem

    User->>DeepmdDataSystem: Initialize with batch_size rule ("max" or "filter")
    DeepmdDataSystem->>DeepmdDataSystem: Parse batch_size string
    alt "max" rule
        DeepmdDataSystem->>DeepmdDataSystem: For each system, compute batch_size = max(1, rule_value // natoms)
    else "filter" rule
        DeepmdDataSystem->>DeepmdDataSystem: Remove systems with natoms > rule_value
        DeepmdDataSystem->>DeepmdDataSystem: If no systems left, raise error
        DeepmdDataSystem->>DeepmdDataSystem: For each remaining system, compute batch_size = max(1, rule_value // natoms)
    end
    DeepmdDataSystem-->>User: Data system initialized with new batch size logic
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155-155: Yoda condition detected

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Actionable comments posted: 2

📜 Review details

Configuration used: CodeRabbit UI
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📥 Commits

Reviewing files that changed from the base of the PR and between 91ebe34 and 6801820.

📒 Files selected for processing (1)
  • deepmd/utils/data_system.py (1 hunks)
🧰 Additional context used
🪛 Ruff (0.12.2)
deepmd/utils/data_system.py

155-155: Yoda condition detected

Rewrite as words[0] == "max"

(SIM300)


168-168: Yoda condition detected

Rewrite as words[0] == "filter"

(SIM300)


182-182: No explicit stacklevel keyword argument found

Set stacklevel=2

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Codecov Report

❌ Patch coverage is 5.40541% with 35 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.30%. Comparing base (88b71e8) to head (b5fb3c2).
⚠️ Report is 71 commits behind head on devel.

Files with missing lines Patch % Lines
deepmd/utils/data_system.py 5.40% 35 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##            devel    #4876      +/-   ##
==========================================
- Coverage   84.34%   84.30%   -0.04%     
==========================================
  Files         702      702              
  Lines       68585    68621      +36     
  Branches     3573     3572       -1     
==========================================
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@njzjz njzjz requested a review from caic99 August 10, 2025 18:47
@njzjz njzjz enabled auto-merge August 11, 2025 13:36
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Merged via the queue into deepmodeling:devel with commit cefce47 Aug 12, 2025
60 checks passed
@OutisLi OutisLi deleted the pr/batch_size branch September 17, 2025 08:08
ChiahsinChu pushed a commit to ChiahsinChu/deepmd-kit that referenced this pull request Dec 17, 2025
…tem (deepmodeling#4876)

# Fix: support "max:N" and "filter:N" batch_size rules in
DeepmdDataSystem

## Problem

- Using `batch_size: "max:..."` or `"filter:..."` in configs caused:
- `RuntimeError: unknown batch_size rule max` during the PyTorch path
(neighbor statistics).
- Docs mention these rules and PyTorch `DpLoaderSet` already supports
them, so behavior was inconsistent across layers.

## Cause

- The common data layer `DeepmdDataSystem` only implemented `"auto"` and
`"mixed"` for string `batch_size`, missing `"max"` and `"filter"`.
- PT training performs neighbor statistics via `DeepmdDataSystem` before
real training, so it failed early when those rules were used.

## Fix

- Implement `"max:N"` and `"filter:N"` in `DeepmdDataSystem.__init__` to
mirror `DpLoaderSet` semantics:
- `max:N`: per-system `batch_size = max(1, N // natoms)` so `batch_size
* natoms <= N`.
- `filter:N`: drop systems with `natoms > N` (warn if any removed; error
if none left), then set per-system `batch_size` as in `max:N`.
- After filtering, update `self.data_systems`, `self.system_dirs`, and
`self.nsystems` before computing other metadata.

## Impact

- Aligns the common layer behavior with PyTorch `DpLoaderSet` and with
the documentation.
- Prevents PT neighbor-stat crashes with configs using
`"max"`/`"filter"`.

## Compatibility

- No change to numeric `batch_size` or existing
`"auto"/"auto:N"/"mixed:N"` rules.
- TF/PT/PD paths now accept the same `batch_size` rules consistently in
the common layer.

## Files Changed

- `deepmd/utils/data_system.py`: add parsing branches for `"max:N"` and
`"filter:N"` in `DeepmdDataSystem.__init__`.

```python
elif "max" == words[0]:
                # Determine batch size so that batch_size * natoms <= rule, at least 1
                if len(words) != 2:
                    raise RuntimeError("batch size must be specified for max systems")
                rule = int(words[1])
                bs = []
                for ii in self.data_systems:
                    ni = ii.get_natoms()
                    bsi = rule // ni
                    if bsi == 0:
                        bsi = 1
                    bs.append(bsi)
                self.batch_size = bs
            elif "filter" == words[0]:
                # Remove systems with natoms > rule, then set batch size like "max:rule"
                if len(words) != 2:
                    raise RuntimeError("batch size must be specified for filter systems")
                rule = int(words[1])
                filtered_data_systems = []
                filtered_system_dirs = []
                for sys_dir, data_sys in zip(self.system_dirs, self.data_systems):
                    if data_sys.get_natoms() <= rule:
                        filtered_data_systems.append(data_sys)
                        filtered_system_dirs.append(sys_dir)
                if len(filtered_data_systems) == 0:
                    raise RuntimeError(f"No system left after removing systems with more than {rule} atoms")
                if len(filtered_data_systems) != len(self.data_systems):
                    warnings.warn(f"Remove {len(self.data_systems) - len(filtered_data_systems)} systems with more than {rule} atoms")
                self.data_systems = filtered_data_systems
                self.system_dirs = filtered_system_dirs
                self.nsystems = len(self.data_systems)
                bs = []
                for ii in self.data_systems:
                    ni = ii.get_natoms()
                    bsi = rule // ni
                    if bsi == 0:
                        bsi = 1
                    bs.append(bsi)
                self.batch_size = bs
```

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Added support for "max" and "filter" batch size rules, allowing more
flexible control over batch sizing and filtering of data systems based
on atom counts.
* **Bug Fixes**
* Improved error handling for incorrect batch size string formats and
cases where no systems remain after filtering.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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